1K4D

Potassium Channel KcsA-Fab complex in low concentration of K+

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

Chemistry of ion coordination and hydration revealed by a K+ channel-Fab complex at 2.0 A resolution.

Zhou, Y., Morais-Cabral, J.H., Kaufman, A., MacKinnon, R.

(2001) Nature 414: 43-48

  • DOI: 10.1038/35102009
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Ion transport proteins must remove an ion's hydration shell to coordinate the ion selectively on the basis of its size and charge. To discover how the K+ channel solves this fundamental aspect of ion conduction, we solved the structure of the KcsA K+ ...

    Ion transport proteins must remove an ion's hydration shell to coordinate the ion selectively on the basis of its size and charge. To discover how the K+ channel solves this fundamental aspect of ion conduction, we solved the structure of the KcsA K+ channel in complex with a monoclonal Fab antibody fragment at 2.0 A resolution. Here we show how the K+ channel displaces water molecules around an ion at its extracellular entryway, and how it holds a K+ ion in a square antiprism of water molecules in a cavity near its intracellular entryway. Carbonyl oxygen atoms within the selectivity filter form a very similar square antiprism around each K+ binding site, as if to mimic the waters of hydration. The selectivity filter changes its ion coordination structure in low K+ solutions. This structural change is crucial to the operation of the selectivity filter in the cellular context, where the K+ ion concentration near the selectivity filter varies in response to channel gating.

    Organizational Affiliation: 

    Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, New Haven, Connecticut 06520, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
antibody Fab fragment heavy chain
A
219Mus musculusMutation(s): 0 
Gene Names: Ighg1 (Igh-4)
Membrane protein
mpstruct		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Channels: Potassium, Sodium, & Proton Ion-Selective		Protein: 
KcsA Potassium channel, H+ gated
Find proteins for P01868 (Mus musculus)
Go to UniProtKB:  P01868
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
antibody Fab fragment light chain
B
212Mus musculusMutation(s): 0 
Gene Names: Igkc
Membrane protein
mpstruct		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Channels: Potassium, Sodium, & Proton Ion-Selective		Protein: 
KcsA Potassium channel, H+ gated
Find proteins for P01837 (Mus musculus)
Go to UniProtKB:  P01837
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
potassium channel KcsA
C
124Streptomyces lividansMutation(s): 2 
Gene Names: kcsA (skc1)
Membrane protein
mpstruct		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Channels: Potassium, Sodium, & Proton Ion-Selective		Protein: 
KcsA Potassium channel, H+ gated
Find proteins for P0A334 (Streptomyces lividans)
Go to UniProtKB:  P0A334
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K
Download SDF File 
Download CCD File 
C
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA
Download SDF File 
Download CCD File 
C
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
DGA
Query on DGA
Download SDF File 
Download CCD File 
C
DIACYL GLYCEROL
C39 H76 O5
UHUSDOQQWJGJQS-QNGWXLTQSA-N
 Ligand Interaction
F09
Query on F09
Download SDF File 
Download CCD File 
C
NONAN-1-OL
C9 H20 O
ZWRUINPWMLAQRD-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.218 
  • Space Group: I 4
Unit Cell:
Length (Å)Angle (°)
a = 155.290α = 90.00
b = 155.290β = 90.00
c = 75.740γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
AMoREphasing
DENZOdata reduction

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-11-14
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2011-11-16
    Type: Atomic model